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- PDB-4ay8: SeMet-derivative of a methyltransferase from M. mazei -

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Basic information

Entry
Database: PDB / ID: 4ay8
TitleSeMet-derivative of a methyltransferase from M. mazei
ComponentsMETHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


uroporphyrinogen decarboxylase activity / porphyrin-containing compound biosynthetic process / methanogenesis / methyltransferase activity / one-carbon metabolic process / methylation / metal ion binding
Similarity search - Function
Methyltransferase MtaA/CmuA / : / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / Methylcobalamin: Coenzyme M methyltransferase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHoeppner, A. / Thomas, F. / Rueppel, A. / Hensel, R. / Blankenfeldt, W. / Bayer, P. / Faust, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the Corrinoid:Coenzyme M Methyltransferase Mtaa from Methanosarcina Mazei
Authors: Hoeppner, A. / Thomas, F. / Rueppel, A. / Hensel, R. / Blankenfeldt, W. / Bayer, P. / Faust, A.
History
DepositionJun 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE
B: METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1979
Polymers75,4802
Non-polymers7187
Water6,648369
1
A: METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0664
Polymers37,7401
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1325
Polymers37,7401
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.210, 125.210, 38.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE / CORRINOID COENZYME M METHYLTRANSFERASE MTAA


Mass: 37739.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PXZ6, EC: 2.1.1.247

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 65% MPD

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.896
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.896 Å / Relative weight: 1
ReflectionResolution: 2.1→38.9 Å / Num. obs: 39734 / % possible obs: 99.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 10.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→33.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.073 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17659 1995 5 %RANDOM
Rwork0.14604 ---
obs0.14755 37708 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 36 369 5455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225165
X-RAY DIFFRACTIONr_bond_other_d00.023476
X-RAY DIFFRACTIONr_angle_refined_deg1.1822.0087018
X-RAY DIFFRACTIONr_angle_other_deg0.83738617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3855678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00425.455176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90915894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2221522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215648
X-RAY DIFFRACTIONr_gen_planes_other00.02866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4941.53396
X-RAY DIFFRACTIONr_mcbond_other0.1071.51362
X-RAY DIFFRACTIONr_mcangle_it0.96625494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90731769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1434.51524
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 145 -
Rwork0.211 2755 -
obs--98.27 %

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